Input and runtime details for job 8257533 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 8257533 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:34:31 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:34:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:30:38 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:30:45 CET 2018
	Job Completed		@ Fri Feb 16 22:31:01 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

Description of the job

LhrA2

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_003210 Listeria monocytogenes EGD-e

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
21	0.003699	0.4469	lmo2681	kdpB	-18.50	0.020601	185 -- 204	154 -- 173	potassium-transporting ATPase subunit B	_____________184__________________205\n_____________\|____________________\|\n5'-GCA...UUUCA____________________UGGAA...AUG-3'\n______________AAUGAGGUGAAUGGAAAUGA\n______________\|\|\|\|\|\|:\|\|\|\|\|\|:\|\|\|::\|\n______________UUACUCUACUUACUUUUGUU\n3'-GUU...GCCGG____________________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________174__________________153\n	197 -- 203	155 -- 161	-22.9313 kcal/mol	3.41 kcal/mol	0.959215 kcal/mol	184 205@LB@ \| \|@LB@5'-GCA...UUUCA UGGAA...AUG-3'@LB@ AAUGAGGUGAAUGGAAAUGA@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|:\|\|\|::\|@LB@ UUACUCUACUUACUUUUGUU@LB@3'-GUU...GCCGG UAUUA...GGA-5'@LB@ \| \|@LB@ 174 153@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -22.9313 kcal/mol@LB@Unfolding Energy - mRNA 3.41 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 185 -- 204@LB@Position - sRNA 154 -- 173@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
22	0.003708	0.4469	lmo1689	N/A	-20.94	0.006216	185 -- 218	155 -- 186	A/G-specific adenine glycosylase	_____________184________________________________219\n_____________\|__________________________________\|\n5'-UGA...UAUUA________A__GGAA_______AA________G_CUAAC...CGU-3'\n______________GAAUUACG_GG____AAUGAGA__AAUGAAGA_A\n______________\|\|\|:\|\|\|:_\|\|____\|\|\|\|\|\|\|__\|\|\|\|\|\|:\|_\|\n______________CUUGAUGU_CC____UUACUCU__UUACUUUU_U\n3'-GUU...CUGUA________G__GG_________AC________G_UUAUU...GGA-5'\n_____________\|__________________________________\|\n_____________187________________________________154\n	210 -- 216	157 -- 163	-27.9128 kcal/mol	3.65812 kcal/mol	9.66922 kcal/mol	184 219@LB@ \| \|@LB@5'-UGA...UAUUA A GGAA AA G CUAAC...CGU-3'@LB@ GAAUUACG GG AAUGAGA AAUGAAGA A@LB@ \|\|\|:\|\|\|: \|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\| \|@LB@ CUUGAUGU CC UUACUCU UUACUUUU U@LB@3'-GUU...CUGUA G GG AC G UUAUU...GGA-5'@LB@ \| \|@LB@ 187 154@LB@@LB@@LB@Energy -20.94 kcal/mol@LB@Hybridization Energy -27.9128 kcal/mol@LB@Unfolding Energy - mRNA 3.65812 kcal/mol@LB@Unfolding Energy - sRNA 9.66922 kcal/mol@LB@@LB@Position - mRNA 185 -- 218@LB@Position - sRNA 155 -- 186@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 157 -- 163@LB@
63	0.01551	0.6624	lmo2613	rplO	-17.63	0.030853	185 -- 213	177 -- 203	50S ribosomal protein L15	_____________184______214\n_____________\|________\|\n5'-AAU...AUUCG________UCACU...GCG-3'\n______________UGGGAUGA\n______________:\|\|\|\|\|\|\|\n______________GCCCUACU\n3'-GUU...GUAUU________CCGUA...GGA-5'\n_____________\|________\|\n_____________204______176\n	98 -- 104	198 -- 204	-11.9514 kcal/mol	5.35707 kcal/mol	0.374397 kcal/mol	184 214@LB@ \| \|@LB@5'-AAU...AUUCG UCACU...GCG-3'@LB@ UGGGAUGA@LB@ :\|\|\|\|\|\|\|@LB@ GCCCUACU@LB@3'-GUU...GUAUU CCGUA...GGA-5'@LB@ \| \|@LB@ 204 176@LB@@LB@@LB@Energy -17.63 kcal/mol@LB@Hybridization Energy -11.9514 kcal/mol@LB@Unfolding Energy - mRNA 5.35707 kcal/mol@LB@Unfolding Energy - sRNA 0.374397 kcal/mol@LB@@LB@Position - mRNA 185 -- 213@LB@Position - sRNA 177 -- 203@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 198 -- 204@LB@
66	0.01668	0.6733	lmo0959	N/A	-18.16	0.024105	185 -- 212	177 -- 206	undacaprenyl-phosphate N-acetylglucosaminyltransferase	_____________184________________213\n_____________\|__________________\|\n5'-GAA...AAGUA_____________A____AUUUG...CAG-3'\n______________UAAUGAGAUGAGU_AAAA\n______________:\|\|\|\|\|\|\|\|\|\|:\|_\|\|\|\|\n______________GUUACUCUACUUA_UUUU\n3'-GUU...UGCCG_____________C____GUUUA...GGA-5'\n_____________\|__________________\|\n_____________207________________176\n	169 -- 175	162 -- 168	-15.497 kcal/mol	1.5517 kcal/mol	0.933292 kcal/mol	184 213@LB@ \| \|@LB@5'-GAA...AAGUA A AUUUG...CAG-3'@LB@ UAAUGAGAUGAGU AAAA@LB@ :\|\|\|\|\|\|\|\|\|\|:\| \|\|\|\|@LB@ GUUACUCUACUUA UUUU@LB@3'-GUU...UGCCG C GUUUA...GGA-5'@LB@ \| \|@LB@ 207 176@LB@@LB@@LB@Energy -18.16 kcal/mol@LB@Hybridization Energy -15.497 kcal/mol@LB@Unfolding Energy - mRNA 1.5517 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 185 -- 212@LB@Position - sRNA 177 -- 206@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 162 -- 168@LB@
81	0.02179	0.6733	lmo0087	N/A	-17.84	0.027970	185 -- 226	166 -- 207	lmo0087	_____________184____________________227\n_____________\|______________________\|\n5'-ACU...AUUAU___AU____G____________AACCU...AUC-3'\n______________UGA__UGGA_GAGAGCAAAUGA\n______________\|\|\|__\|\|:\|_\|\|:\|:\|\|\|\|\|:\|\n______________ACU__ACUU_CUUUUGUUUAUU\n3'-GUU...CGGUU___CU____A____________ACUAA...GGA-5'\n_____________\|______________________\|\n_____________208____________________165\n	195 -- 201	153 -- 159	-17.3998 kcal/mol	2.37482 kcal/mol	5.01319 kcal/mol	184 227@LB@ \| \|@LB@5'-ACU...AUUAU AU G AACCU...AUC-3'@LB@ UGA UGGA GAGAGCAAAUGA@LB@ \|\|\| \|\|:\| \|\|:\|:\|\|\|\|\|:\|@LB@ ACU ACUU CUUUUGUUUAUU@LB@3'-GUU...CGGUU CU A ACUAA...GGA-5'@LB@ \| \|@LB@ 208 165@LB@@LB@@LB@Energy -17.84 kcal/mol@LB@Hybridization Energy -17.3998 kcal/mol@LB@Unfolding Energy - mRNA 2.37482 kcal/mol@LB@Unfolding Energy - sRNA 5.01319 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 166 -- 207@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 153 -- 159@LB@
96	0.02498	0.6733	lmo1278	clpQ	-17.33	0.035430	185 -- 216	173 -- 203	ATP-dependent protease peptidase subunit	_____________184_____217\n_____________\|_______\|\n5'-AAA...UCAAC_______AAAAG...UGA-3'\n______________AUGACGG\n______________\|\|:\|\|\|\|\n______________UAUUGCC\n3'-GUU...AUACG_______CUACU...GGA-5'\n_____________\|_______\|\n_____________204_____172\n	238 -- 244	203 -- 209	-8.20287 kcal/mol	1.40847 kcal/mol	0.374301 kcal/mol	184 217@LB@ \| \|@LB@5'-AAA...UCAAC AAAAG...UGA-3'@LB@ AUGACGG@LB@ \|\|:\|\|\|\|@LB@ UAUUGCC@LB@3'-GUU...AUACG CUACU...GGA-5'@LB@ \| \|@LB@ 204 172@LB@@LB@@LB@Energy -17.33 kcal/mol@LB@Hybridization Energy -8.20287 kcal/mol@LB@Unfolding Energy - mRNA 1.40847 kcal/mol@LB@Unfolding Energy - sRNA 0.374301 kcal/mol@LB@@LB@Position - mRNA 185 -- 216@LB@Position - sRNA 173 -- 203@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 203 -- 209@LB@
151	0.03914	0.6976	lmo1466	N/A	-16.64	0.048271	185 -- 226	158 -- 202		_____________184_______________________________________________227\n_____________\|_________________________________________________\|\n5'-UGA...UUAGA____AGA__A_______A_____________________________G_UUGGU...UUC-3'\n______________GAGG___CA_AGAUGUG_AACUA____GCCAA_GA____AAUGGAGA_A\n______________\|\|\|\|___\|\|_\|\|\|::\|\|_\|\|\|\|\|____\|\|\|\|\|_\|\|____\|\|\|\|:\|:\|_\|\n______________CUCC___GU_UCUGUAC_UUGAU____CGGUU_CU____UUACUUUU_U\n3'-GUU...CCCUA_________A_____________GUGC_____A__CUAC________G_UUAUU...GGA-5'\n_____________\|_________________________________________________\|\n_____________203_______________________________________________157\n	218 -- 224	157 -- 163	-27.6675 kcal/mol	5.9878 kcal/mol	13.9822 kcal/mol	184 227@LB@ \| \|@LB@5'-UGA...UUAGA AGA A A G UUGGU...UUC-3'@LB@ GAGG CA AGAUGUG AACUA GCCAA GA AAUGGAGA A@LB@ \|\|\|\| \|\| \|\|\|::\|\| \|\|\|\|\| \|\|\|\|\| \|\| \|\|\|\|:\|:\| \|@LB@ CUCC GU UCUGUAC UUGAU CGGUU CU UUACUUUU U@LB@3'-GUU...CCCUA A GUGC A CUAC G UUAUU...GGA-5'@LB@ \| \|@LB@ 203 157@LB@@LB@@LB@Energy -16.64 kcal/mol@LB@Hybridization Energy -27.6675 kcal/mol@LB@Unfolding Energy - mRNA 5.9878 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 158 -- 202@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 157 -- 163@LB@
30	0.00607	0.5445	lmo0619	N/A	-20.15	0.009257	186 -- 283	154 -- 223	lmo0619	_____________185_____________________________________________________________________________________________________284\n_____________\|_______________________________________________________________________________________________________\|\n5'-UAU...AACAG_____G__GC____CUU___________AAAAAG_____AGUAAAUUACUUCA_______AAAAAAGCGACCAAUU_________GUAUUA____________GGCGG...CAA-3'\n______________UCGGG_GU____GC___AU_GGAUGGGG______AGACA______________UGAAUUA________________UAC_GCCAA_______GAUGAAAACGA\n______________\|\|\|\|\|_\|:____\|\|___\|:_\|\|\|\|\|:\|\|______\|\|\|\|\|______________\|\|\|\|:\|\|________________:\|\|_\|\|\|\|\|_______:\|\|\|\|\|\|\|\|:\|\n______________AGCCC_CG____CG___UG_CCUACUCC______UCUGU______________ACUUGAU________________GUG_CGGUU_______UUACUUUUGUU\n3'-GUU...GUACA_____G__GAUA__UAU__C________GUA________________________________________________C_____ACUCUAC___________UAUUA...GGA-5'\n_____________\|_______________________________________________________________________________________________________\|\n_____________224_____________________________________________________________________________________________________153\n	277 -- 283	154 -- 160	-48.8019 kcal/mol	13.571 kcal/mol	22.2956 kcal/mol	185 284@LB@ \| \|@LB@5'-UAU...AACAG G GC CUU AAAAAG AGUAAAUUACUUCA AAAAAAGCGACCAAUU GUAUUA GGCGG...CAA-3'@LB@ UCGGG GU GC AU GGAUGGGG AGACA UGAAUUA UAC GCCAA GAUGAAAACGA@LB@ \|\|\|\|\| \|: \|\| \|: \|\|\|\|\|:\|\| \|\|\|\|\| \|\|\|\|:\|\| :\|\| \|\|\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ AGCCC CG CG UG CCUACUCC UCUGU ACUUGAU GUG CGGUU UUACUUUUGUU@LB@3'-GUU...GUACA G GAUA UAU C GUA C ACUCUAC UAUUA...GGA-5'@LB@ \| \|@LB@ 224 153@LB@@LB@@LB@Energy -20.15 kcal/mol@LB@Hybridization Energy -48.8019 kcal/mol@LB@Unfolding Energy - mRNA 13.571 kcal/mol@LB@Unfolding Energy - sRNA 22.2956 kcal/mol@LB@@LB@Position - mRNA 186 -- 283@LB@Position - sRNA 154 -- 223@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 154 -- 160@LB@
18	0.003504	0.4469	lmo0129	N/A	-18.06	0.025228	187 -- 226	176 -- 203	N-acetylmuramoyl-L-alanine amidase	_____________186____________227\n_____________\|______________\|\n5'-UUU...GUCAG______________AAAAC...AAC-3'\n______________GAGA_GGAUGAGGA\n______________\|\|\|\|_\|:\|\|\|\|::\|\n______________CUCU_CUUACUUUU\n3'-GUU...GGUUA____A_________GUUUA...GGA-5'\n_____________\|______________\|\n_____________204____________175\n	189 -- 195	157 -- 163	-12.9517 kcal/mol	0.542108 kcal/mol	0.904482 kcal/mol	186 227@LB@ \| \|@LB@5'-UUU...GUCAG AAAAC...AAC-3'@LB@ GAGA GGAUGAGGA@LB@ \|\|\|\| \|:\|\|\|\|::\|@LB@ CUCU CUUACUUUU@LB@3'-GUU...GGUUA A GUUUA...GGA-5'@LB@ \| \|@LB@ 204 175@LB@@LB@@LB@Energy -18.06 kcal/mol@LB@Hybridization Energy -12.9517 kcal/mol@LB@Unfolding Energy - mRNA 0.542108 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 187 -- 226@LB@Position - sRNA 176 -- 203@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 157 -- 163@LB@
41	0.008795	0.5772	lmo1984	ilvB	-19.06	0.015768	187 -- 229	157 -- 201	acetolactate synthase	_____________186____________________________________________230\n_____________\|______________________________________________\|\n5'-AUU...AAAAA_______G___A______UUG_____A_________CA________AGCGA...ACA-3'\n______________AUGAGGU_AUA_GCGUGA___AUACG__CGA__AGA__AAUGAAAA\n______________\|\|\|\|\|\|:_\|\|\|_:\|:\|\|\|___\|:\|\|\|__\|:\|__\|\|\|__\|\|\|\|\|\|\|\|\n______________UACUCCG_UAU_UGUACU___UGUGC__GUU__UCU__UUACUUUU\n3'-GUU...UGCCC___________C______UGA_____CG___AC___AC________GUUUA...GGA-5'\n_____________\|______________________________________________\|\n_____________202____________________________________________156\n	223 -- 229	157 -- 163	-31.6948 kcal/mol	5.6221 kcal/mol	13.9999 kcal/mol	186 230@LB@ \| \|@LB@5'-AUU...AAAAA G A UUG A CA AGCGA...ACA-3'@LB@ AUGAGGU AUA GCGUGA AUACG CGA AGA AAUGAAAA@LB@ \|\|\|\|\|\|: \|\|\| :\|:\|\|\| \|:\|\|\| \|:\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UACUCCG UAU UGUACU UGUGC GUU UCU UUACUUUU@LB@3'-GUU...UGCCC C UGA CG AC AC GUUUA...GGA-5'@LB@ \| \|@LB@ 202 156@LB@@LB@@LB@Energy -19.06 kcal/mol@LB@Hybridization Energy -31.6948 kcal/mol@LB@Unfolding Energy - mRNA 5.6221 kcal/mol@LB@Unfolding Energy - sRNA 13.9999 kcal/mol@LB@@LB@Position - mRNA 187 -- 229@LB@Position - sRNA 157 -- 201@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 157 -- 163@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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